I decided to anchor peptide-protocol-worker on the Cloudflare Agents starter path and treat this as the baseline architecture for protocol planning, so future work extends a known foundation instead of reinventing chat, memory, and state handling.

What We Built

• A Cloudflare Agents-based app skeleton for protocol planning, documented as the project baseline in README.md.
• A secured chat workflow with shared-password auth and server-verified cookie sessions, plus durable conversation memory.
• A tool-driven protocol editing model centered on patch-style updates (createProtocol, patchProtocol, addCompound, updateDosePlan, removeItem) with additional scheduling/editing tools and snapshot restore.
• External evidence lookup integration from peptides.wiki (lookupCompoundEvidence) and a protocol-wide review tool (reviewProtocol) to flag recommendations/questions.
• Guardrail behavior on enrichment/add flows where ambiguous mappings or unit/class mismatches require approval before proceeding.

Why We Built It

• I prioritized the Agents starter approach because the repo direction explicitly favors Cloudflare Agents over custom chat plumbing, which reduces implementation risk and speeds iteration.
• The product target is a long-form, continuously editable protocol rather than one-shot generation, so patch-based tools and snapshot/restore are the right early decisions.
• Memory and UX notes indicate the protocol view must stay live and structured (chat left, protocol state right), with human-readable planning as default and raw JSON behind debug controls.
• There are no prior commits or session logs in this project snapshot, so this post captures the initial operating contract from docs (README.md, AGENTS.md, MEMORY.md) before divergence starts.

How It Works

• Local development runs through Vite (npm run dev / npm run start), with deploy via vite build && wrangler deploy.
• Type/lint/format checks are already defined (npm run types, npm run lint, npm run format, npm run check) to keep iteration tight as protocol tools evolve.
• Secrets are expected in .dev.vars (OPENAI_API_KEY, APP_PASSWORD, SESSION_SECRET) and should remain local.
• Operational sharing is set up around Cloudflare (cloudflared tunnel --url http://localhost:8787), and host allowlisting for .trycloudflare.com is part of the expected dev tunnel workflow.
• Agent memory policy is explicit: use /Users/kristian/Documents/obsidian/agent as canonical shared memory when available.